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Indonesian election returns suggest that former Gen. Susilo Bambang Yudhoyono on Monday won a landslide to become president. His domestic success derives from his personal image as being independent of the corrupt political and economic forces that rule the country. More important internationally, Gen. Yudhoyono has vowed to crack down on al Qaeda-linked terrorist groups in Indonesia. His election is a sign of hope in Southeast Asia.

Not only were the archipelago’s voting stations peaceful, but Indonesians soundly rejected Islamic parties at the polls. Gen. Yudhoyono was trained by the U.S. military and promoted through the ranks during the pro-American military government of President Suharto, who squelched Islamist political parties and forced radical imams into exile. Picking a new president with this background reflects Indonesia’s overwhelming moderation and clear rejection of anti-Western Islamist politics.

It is important now for Washington and the West to give soon-to-be President Yudhoyono breathing room to address his nation’s security problems. While the world focuses on the al Qaeda-linked Jemaah Islamiya, most Indonesians are more concerned with separatist violence in some of its provinces. Jemaah Islamiya’s high-publicity bombings have killed more than 200 people, while tens of thousands have been killed in separatist provinces. A majority of Indonesians feel that these rebellions pose the more serious threat to the state. The need to confront this ongoing crisis is why a former general outpolled incumbent President Megawati Sukarnoputri.

A military solution alone will not stabilize Indonesia. The new president will need political settlements in the rebellious provinces. Two sought-after reforms are more local autonomy and control over local resources. As it stands, almost all of the royalties from oil and minerals in the provinces go directly to Jakarta and bypass the locals. Gen. Yudhoyono’s vast public support could provide the political cover needed to challenge the entrenched interests.

While the government will not be excited to give up any of its provincial profits, it will continue to prove impossible to quell violence and undercut independence movements without moving in that direction. Moreover, in the immediate term, reform is good for business. Peace and stability will bring more foreign investment, which Indonesians need to tackle the high unemployment rate.

The most positive news of the Indonesian election is that radical Islam has no traction as a political force in the most populous Muslim nation in the world. The hope is that the landslide election of a secular pro-American leader opens a window for more substantive reform that will make Indonesia more democratic, more egalitarian and thus more stable — which all make it less likely to be a breeding ground for terrorists.